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- PDB-3d2v: Structure of the eukaryotic TPP-specific riboswitch bound to the ... -

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Basic information

Entry
Database: PDB / ID: 3d2v
TitleStructure of the eukaryotic TPP-specific riboswitch bound to the antibacterial compound pyrithiamine pyrophosphate
ComponentsTPP-specific riboswitch
KeywordsRNA / riboswitch / antibiotic / thiamine pyrophosphate / pyrithiamine pyrophosphate / complex
Function / homologyChem-PYI / RNA / RNA (> 10)
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsThore, S. / Frick, C. / Ban, N.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch
Authors: Thore, S. / Frick, C. / Ban, N.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TPP-specific riboswitch
B: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,99914
Polymers49,9182
Non-polymers1,08212
Water9,980554
1
A: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5248
Polymers24,9591
Non-polymers5657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4756
Polymers24,9591
Non-polymers5175
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.790, 110.780, 55.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-164-

HOH

21A-371-

HOH

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Components

#1: RNA chain TPP-specific riboswitch


Mass: 24958.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: In vitro transcription / Production host: cell-free synthesis (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PYI / 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM / PYRITHIAMIN PYROPHOSPHATE


Mass: 419.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N4O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 12-18% 1,6-hexanediol, 0.5 mM spermine, 10 mM magnesium sulfate, 40 mM sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
11,6-hexanediol11
21,6-hexanediol12
3spermine11
4magnesium sulfate11
5magnesium sulfate12
6sodium cacodylate11
7sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 33481 / Num. obs: 33092 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 33.5
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 5.87 / Num. unique all: 2372 / % possible all: 92.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2cky

2cky


Resolution: 2→15 Å / σ(F): 1.36 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1675 5.07 %RANDOM
Rwork0.207 ---
obs0.226 33016 99.07 %-
all-33092 --
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3310 64 554 3928

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